Choosing only Breast cancer in GENIE data

[Shakuntala Baichoo]

Hi!

I want to study one specific gene (e.g. BRCA1) in Breast Cancer in the GENIE cohort. How can I choose Breast cancer before calling "Query gene" in GENIE?

Thanks,

Shakuntala

[Tali Mazor]

Hi Shakuntala,

There are two ways you can do this.

From the homepage when you run a query, there's an option to 'Select Patient/Case Set'. Here you can select Breast Cancer from the dropdown menu:

Once you select this, your query will only run in Breast Cancer samples.

Alternatively, if you want a subset of samples which is not available in that list, you can first explore a study in study view. There, you can apply filters and then use the query box in the upper right to enter your gene of interest and run a query in just those samples you've filtered to:

Slide 16 in this tutorial slide deck shown more detail on this approach: https://genie.cbioportal.org/tutorials#single-study-exploration

I hope this helps!

-Tali

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[Shakuntala Baichoo]

Hi Tali,

Thank you very much for the details. This is really helpful.

Best regards,

Shakuntala